 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 20, 2014 |
| Title |
saliva_HA12 |
| Sample type |
genomic |
| |
|
| Source name |
1 ml saliva, lysed
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
sampling location: San Antonio de los Cobres, Argentina
sampling type: High altitude sample
|
| Treatment protocol |
Storage at room temperature for 2 weeks, 1-3 weeks at 4°C, centrifugation
|
| Growth protocol |
Saliva mixed with equal volume of lysis buffer (Quinque et al. 2006) to allow storage at room temperature
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen DNA Investigator Kit scaled up for 2 ml buffer-saliva mixture
|
| Label |
Cy3,Cy5
|
| Label protocol |
Followed Illumina standard protocol
|
| |
|
| Hybridization protocol |
Followed Illumina standard protocol
|
| Scan protocol |
Followed Illumina standard protocol
|
| Description |
And_S41
|
| Data processing |
Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).
|
| |
|
| Submission date |
Feb 19, 2014 |
| Last update date |
Feb 20, 2014 |
| Contact name |
Christina A Eichstaedt |
| Organization name |
University of Cambridge
|
| Department |
Biological Anthropology
|
| Street address |
Fitzwilliam Street
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QH |
| Country |
Germany |
| |
|
| Platform ID |
GPL13135 |
| Series (1) |
| GSE55175 |
Argentinean high altitude adaptation |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Genotype: AA, AB, BB,or NC (no call) |
| Score |
|
| Theta |
|
| R |
|
| B Allele Freq |
|
| Log R Ratio |
|
| Data table |
| ID_REF |
VALUE |
Score |
Theta |
R |
B Allele Freq |
Log R Ratio |
| rs1000000 |
BB |
0.8375055 |
0.9850642 |
1.548797 |
0.9946218 |
-0.04150472 |
| rs1000002 |
BB |
0.8591028 |
0.970955 |
0.6538274 |
0.9955827 |
-0.3703692 |
| rs10000023 |
AA |
0.8250977 |
0.01939203 |
1.872791 |
0.00 |
-0.02957125 |
| rs1000003 |
AA |
0.9295058 |
0.04248882 |
1.000191 |
0.0006155523 |
-0.1544877 |
| rs10000030 |
BB |
0.5007726 |
0.948643 |
0.6918509 |
0.9623657 |
0.3457178 |
| rs10000037 |
BB |
0.8681842 |
0.9613008 |
0.8993867 |
0.9937323 |
0.03844951 |
| rs10000041 |
AB |
0.8502855 |
0.4375042 |
1.221682 |
0.5388177 |
-0.0686245 |
| rs10000042 |
BB |
0.8005315 |
0.9738833 |
0.9040709 |
1 |
0.01577403 |
| rs10000049 |
AA |
0.8983551 |
0.03359089 |
1.343242 |
0.01322978 |
-0.0157195 |
| rs1000007 |
AA |
0.941943 |
0.002389091 |
1.3474 |
0.00 |
0.01654359 |
| rs10000073 |
AA |
0.9145088 |
0.01867514 |
1.059826 |
0.00 |
0.05410529 |
| rs10000081 |
AA |
0.916678 |
0.03738763 |
0.899527 |
0.00 |
0.04932511 |
| rs10000092 |
AA |
0.8982798 |
0.01796047 |
0.6842345 |
0.00 |
-0.1062288 |
| rs10000105 |
BB |
0.8805913 |
0.9788263 |
1.157631 |
1 |
-0.02744224 |
| rs10000119 |
BB |
0.902257 |
0.9896867 |
1.271124 |
1 |
-0.04010345 |
| rs10000124 |
BB |
0.8189796 |
0.9852039 |
1.309241 |
1 |
-0.09320425 |
| rs10000147 |
AA |
0.4752468 |
0.05079857 |
0.583752 |
0.00 |
0.4559929 |
| rs10000154 |
AA |
0.9396823 |
0.02439555 |
0.8730848 |
0.001643884 |
0.07833245 |
| rs1000016 |
AB |
0.8982587 |
0.5756577 |
0.6468961 |
0.4918477 |
-0.08034422 |
| rs10000160 |
BB |
0.8540631 |
0.9612675 |
0.7338641 |
0.9965881 |
-0.04553138 |
Total number of rows: 731442
Table truncated, full table size 43580 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
|
|
|
|
 |
